P462: IDENTIFICATION OF TARGETED THERAPIES DIRECTED TO ACUTE MYELOID LEUKEMIA MINIMAL RESIDUAL DISEASE
Authors: N. van Gils, F. Kessler, M. Broux, F. Denkers, S. Demeyer, J. Cools, D. C. De Leeuw, J. Janssen, L. Smit
Journal: HemaSphere (2022)

Background: Despite good responses to intensive polychemotherapy in the initial treatment phase, the biggest challenge in the treatment of acute myeloid leukemia (AML) is persistence of residual therapy-resistant cancer cells (measurable residual disease, MRD) that can develop into recurrence. Leukemia cells with stem cell features (“leukemic stem cells”, LSCs) residing within MRD are thought to be at the origin of relapse. Current knowledge gaps on residual leukemic cell persistence and ways to target MRD are hampering progress in development of treatments successfully preventing relapse and increasing AML cure rates. Aims: To identify transcriptional and epigenetic characteristics and vulnerabilities of AML MRD, guiding the design of “targeted” combination treatment strategies that successfully eliminate relapse-initiating cells in individual AML patients. Methods: We developed in vivo patient-derived xenograft (PDX) NOD/SCID/IL2Rγc-deficient (NSG) mouse models mimicking MRD by 1) intravenous (IV) injection of primary AML diagnosis samples and, as soon as leukemic cells were detectable in the peripheral blood, treatment with combination chemotherapy, and 2) IV injection of AML patient samples at the stage of MRD in NSG mice. Moreover, we selected samples from individual AML patients at different time points, diagnosis, MRD and relapse, and purified by flow cytometry the leukemic cells using the leukemia-associated immunophenotype (LAIP) expressed on the AML cells. To elucidate the mutational landscape, transcriptional program and chromatin accessibility involved in development and persistence of MRD, we performed DNA-, RNA- and the assay for transposase-accessible chromatin (ATAC)-sequencing on the purified leukemic cells. Results: We revealed that in patient AML samples at the stage of MRD there is clonogenic capacity of leukemic stem/progenitors (Figure 1A). Treatment with combination chemotherapy significantly reduced leukemic burden in the bone marrow of NSG mice (Figure 1B top). Interestingly, the number of CD34+CD38- leukemic cells in AML1 was hardly affected by chemotherapy, whereas treatment significantly reduced the number of these cells in AML2 (Figure 1B bottom), indicating that leukemic CD34+CD38- cells residing within different patients have a heterogeneous response to polychemotherapy. Injection of AML MRD from several patients resulted in leukemia engraftment (example Figure 1C). For one case, marked as MRD-negative by flow cytometry, we even observed that MRD could initiate high leukemia load in the mice (Figure 1D), while after injection of diagnosis and relapsed AML from the same patient no engraftment was observed. Together, our results implicated that AML cells after therapy, even if the patient is marked as MRD-negative, could have high leukemia-initiating potential, which could have been induced by chemotherapy. Using RNA-sequencing we identified and compared the gene expression profile and chromatin accessibility of leukemic cells at diagnosis, MRD and relapse from patients samples. We identified several genes upregulated in AML MRD cells as compared to diagnosis AML. Moreover, we showed increased chromatin accessibility, indicating open chromatin structure and potential transcriptional activity, at several loci in MRD compared to diagnosis AML, giving opportunities to therapeutically target MRD. Image:Summary/Conclusion: We generated AML MRD PDX mouse models, and identified transcriptional and epigenetic characteristics of AML MRD that might guide the design of “targeted” combination treatment strategies potentially eliminating relapse-initiating cells.